ABSTRACT Altitudinal gradients offer a unique opportunity to understand the drivers of species richness, as mountain regions cover vast areas and contribute disproportionately to global terrestrial biodiversity. However, such gradients are often studied without considering the role of microhabitats, which introduce fine‐scale heterogeneity within coarse macroenvironmental conditions. This heterogeneity may be especially important for microscopic animals, whose distributions and interactions are largely confined to the microhabitat scale. In our study, we investigated altitudinal patterns of microscopic invertebrates (Tardigrada), testing the hypothesis that microhabitat characteristics modulate the effects of macroenvironmental gradients on diversity and community structure. We compiled an extensive inventory of tardigrade taxa inhabiting bryophytes across the Western Alps (Northern Italy) and analysed 546 bryophyte samples collected along a broad altitudinal gradient using DNA metabarcoding to characterise tardigrade communities. For each taxon, we gathered functional trait data to assess how species characteristics influence distribution. We then evaluated the effects of macroenvironmental variables (altitude, vegetation type, slope exposition) and microhabitat‐level traits (bryophyte biological and structural features) using spatially explicit statistical modelling. We found that species richness decreased with altitude, whereas standardised phylogenetic and functional diversity increased, indicating higher redundancy at lower elevations. Our results reveal that tardigrade communities in bryophyte microhabitats are highly heterogeneous, with strong species turnover and prevalent phylogenetic and functional underdispersion. Despite the influence of stochastic processes in shaping their distributions, we show that macroenvironmental variables such as altitude and geographic location drive species turnover, while microhabitat traits govern trait‐based community structure. These findings support the view that microhabitats act as fine‐scale filters modulating the broader effects of altitude on diversity, highlighting the importance of incorporating microhabitat heterogeneity when studying organismal diversity along altitudinal gradients.